Methods are being developed to map the distribution of elements in cells and macromolecular assemblies using the technique of electron- spectroscopic imaging in a scanning transmission electron microscope (STEM) equipped with a cold field-emission gun and a magnetic sector electron spectrometer coupled to a parallel detection system. Mapping single atoms in biological structures is now becoming within the reach of this instrumentation. Imaging can be performed at low dose with dark-field STEM prior to analysis at high dose, so that structures of macromolecular assemblies can be correlated with the numbers of specific atoms that they contain. Measurements confirm theoretical predictions that single atom detection of phosphorus can be realized by using a nanometer diameter probe. Although phosphorus atoms may have moved several nanometers from their original positions due to beam- induced structural degradation, damaged molecules are nevertheless stable enough to be analyzed at 1 or 2 nanometer resolution. Such analyses can only be achieved by means of spectrum-imaging with correction for specimen drift. Optimal strategies for mapping small numbers of phosphorus atoms have been investigated using well characterized specimens of DNA and viruses. Experiments are being designed to map single atoms of other biologically important elements like calcium and iron that also have favorable ionization cross sections. - STEM, scanning transmission electron microscopy, phosphorus, molecular weights, mass maps, microanalysis